Polypharmacology-based kinome screen identifies new regulators of KSHV reactivation

Kaposi's sarcoma-associated herpesvirus (KSHV) causes several human diseases including Kaposi's sarcoma (KS), a leading cause of cancer in Africa and in patients with AIDS. KS tumor cells harbor KSHV predominantly in a latent form, while typically <5% contain lytic replicating virus. Because both latent and lytic stages likely contribute to cancer initiation and progression, continued dissection of host regulators of this biological switch will provide insights into fundamental pathways controlling the KSHV life cycle and related disease pathogenesis. Several cellular protein kinases have been reported to promote or restrict KSHV reactivation, but our knowledge of these signaling mediators and pathways is incomplete. We employed a polypharmacology-based kinome screen to identifiy specific kinases that regulate KSHV reactivation. Those identified by the screen and validated by knockdown experiments included several kinases that enhance lytic reactivation: ERBB2 (HER2 or neu ), ERBB3 (HER3), ERBB4 (HER4), MKNK2 (MNK2), ITK, TEC, and DSTYK (RIPK5). Conversely, ERBB1 (EGFR1 or HER1), MKNK1 (MNK1) and FRK (PTK5) were found to promote the maintenance of latency. Mechanistic characterization of ERBB2 pro-lytic functions revealed a signaling connection between ERBB2 and the activation of CREB1, a transcription factor that drives KSHV lytic gene expression. These studies provided a proof-of-principle application of a polypharmacology-based kinome screen for the study of KSHV reactivation and enabled the discovery of both kinase inhibitors and specific kinases that regulate the KSHV latent-to-lytic replication switch.

Author Summary

Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer particularly prevalent in Africa. In cancer cells, the virus persists in a quiescent form called latency, in which only a few viral genes are made. Periodically, the virus switches into an active replicative cycle in which most of the viral genes are made and new virus is produced. What controls the switch from latency to active replication is not well understood, but cellular kinases, enzymes that control many cellular processes, have been implicated. Using a cell culture model of KSHV reactivation along with an innovative screening method that probes the effects of many cellular kinases simultaneously, we identified drugs that significantly limit KSHV reactivation, as well as specific kinases that either enhance or restrict KSHV replicative cycle. Among these were the ERBB kinases which are known to regulate growth of cancer cells. Understanding how these and other kinases contribute to the switch leading to production of more infectious virus helps us understand the mediators and mechanisms of KSHV diseases. Additionally, because kinase inhibitors are proving to be effective for treating other diseases including some cancers, identifying ones that restrict KSHV replicative cycle may lead to new approaches to treating KSHV-related diseases.

Abstract B32: High-throughput chemical screening reveals YAP-mediated alterations in drug sensitivities

The Hippo pathway is evolutionarily conserved and plays a critical role in determining organ size and in tumorigenesis. Aberrant genetic alterations in the Hippo pathway genes including LATS1/2, NF2, and STK11, as well as increased expression and activity of YAP have been found in some human cancers. Loss of function of Hippo genes results in increased nuclear localization of YAP, which promotes cell proliferation, migration, and invasion. Despite our increasing understanding of molecular phenotypes associated with Hippo aberration and excess YAP activity, there are as yet no FDA-approved therapies targeting this pathway, representing a large, unmet patient need. Previous work from our lab has established an additional role for the pathway in altering cellular response to gemcitabine in pancreatic cancer (PNAS 2017). To uncover therapeutic vulnerabilities caused by increased YAP activity, we performed a quantitative, high-throughput screen using the Mechanism Interrogation PlatE (MIPE) library of compounds. All the drugs in this library are relevant for clinical use in cancer and have known mechanisms of action. Annotated gene families represented in the MIPE library include kinases, GPCRs, and ion channels as well as broad cellular mechanisms including modulators of nuclear receptor transcription factors, lipid metabolism, histone epigenetic machinery, and apoptosis. The screen was carried out in twenty 1,536-well plates consisting of 2,154 compounds at nine different doses on both Panc02.13 cells expressing GFP or constitutively active YAP (YAPS6A). Preliminary data have confirmed our previous work in YAP’s role in increasing sensitivity to gemcitabine and several other chemotherapeutics. Pathway enrichment analysis of drugs based on similar mechanism of action allowed us to identify specific signaling nodes and cellular processes that present points of vulnerability or resistance caused by excess YAP activity. We discovered a profound increase in cellular resistance to MEK inhibitors. AC50 values for seventeen out of eighteen MEK inhibitors tested were on average more than four-fold higher in YAPS6A-expressing cells. We have validated these results in several other pancreatic cell lines in both 2D and 3D spheroid assays. Molecular analysis revealed that nuclear YAP causes sustained PI3K/AKT activation, providing a plausible compensatory pathway for cell survival. Moreover, treatment with PI3K/AKT inhibitors can abrogate this YAP-induced resistance to MEK inhibitors. Overall our data are consistent with previous findings that increases in PI3K and AKT signaling function as an escape mechanism to MEK inhibition. Our data suggest that increased YAP activity may represent a distinct molecular mechanism for how this escape is accomplished in refractory cancers. Cotargeting PI3K/AKT may thus provide therapeutic options for patients carrying mutations in Hippo pathway genes.

Citation Format: Andrew J. Bondesson, Aya Miyaki, Stella Shin, Michele Ceribelli, Craig J. Thomas, Taran S. Gujral. High-throughput chemical screening reveals YAP-mediated alterations in drug sensitivities [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr B32.

Profiling phospho-signaling networks in breast cancer using reverse-phase protein arrays

Measuring the states of cell signaling pathways in tumor samples promises to advance the understanding of oncogenesis and identify response biomarkers. Here, we describe the use of Reverse Phase Protein Arrays (RPPAs or RPLAs) to profile signaling proteins in 56 breast cancers and matched normal tissue. In RPPAs, hundreds to thousands of lysates are arrayed in dense regular grids and each grid is probed with a different antibody (100 in the current work, of which 71 yielded strong signals with breast tissue). Although RPPA technology is quite widely used, measuring changes in phosphorylation reflective of protein activation remains challenging. Using repeat deposition and well-validated antibodies, we show that diverse patterns of phosphorylation can be monitored in tumor samples and changes mapped onto signaling networks in a coherent fashion. The patterns are consistent with biomarker-based classification of breast cancers and known mechanisms of oncogenesis. We explore in detail one tumor-associated pattern that involves changes in the abundance of the Axl receptor tyrosine kinase (RTK) and phosphorylation of the cMet RTK. Both cMet and Axl have been implicated in breast cancer, or in resistance to anticancer drugs, but the two RTKs are not known to be linked functionally. Protein depletion and overexpression studies in a 'triple-negative' breast cell line reveal cross talk between Axl and cMet involving Axl-mediated modification of cMet, a requirement for cMet in efficient and timely signal transduction by the Axl ligand Gas6 and the potential for the two receptors to interact physically. These findings have potential therapeutic implications, as they imply that bi-specific receptor inhibitors (for example, ATP-competitive small-kinase inhibitors such as GSK1363089, BMS-777607 or MP470) may be more efficacious than the mono-specific therapeutic antibodies currently in development (for example, Onartuzumab).